Researchers believe that thousands of genes and their products (i.e., RNA and proteins) in a given living organism function in a complicated and orchestrated way. However, traditional methods in molecular biology generally work on a “one gene in one experiment” basis, which means that the throughput is very limited and the “whole picture” of gene function is hard to obtain. In the past several years, a new technology, called DNA microarray, has attracted tremendous interests among biologists. This technology attempts to monitor the whole genome on a single chip so that researchers can have a better picture of the interactions among thousands of genes simultaneously.
An array is an orderly arrangement of samples. It provides a medium for matching known and unknown DNA samples based on base-pairing rules and automating the process of identifying the unknowns. An array experiment can make use of common assay systems, such as microplates or standard blotting membranes, and can be created by hand or make use of robotics to deposit the sample. In general, arrays are described as macroarrays or microarrays, the difference being the size of the sample spots. Macroarrays contain sample spot sizes of about 300 microns or larger and can be easily imaged by existing gel and blot scanners. The sample spot sizes in microarray are typically less than 200 microns in diameter and these arrays usually contains thousands of spots. Microarrays require specialized robotics and imaging equipment that generally are not commercially available as a complete system.
DNA microarray, or DNA chips, are fabricated by high-speed robotics, generally on glass but sometimes on nylon substrates, for which probes with known identity are used to determine complementary binding, thus allowing massively parallel gene expression and gene discovery studies. An experiment with a single DNA chip can provide researchers information on thousands of genes simultaneously—a dramatic increase in throughput.
In the process of manufacturing DNA micro array and synthetic DNA strands, an image is repeatedly projected on the substrate. While the substrate is not moved during processing, the images need to be kept stable across different phases of exposure that may last a total of 4–8 hours. During this time, the optical system drifts from its reference state because, for instance, of changes in the environment. It is not practical to try to completely eliminate these drifts. As such, there is a need for a feedback system to stabilize or lock the image used in the DNA micro array and strands manufacturing.